Ligation-anchored PCR unveils immune repertoire of TCR-betafrom whole blood

Fan Gao1# & Kai Wang 1, 2*

1: Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90089, USA

2: Department of Psychiatry, University of Southern California, Los Angeles, CA 90089, USA

#: Current address: The Picower Institute for Learning and Memory, MIT, Boston, MA 02139, USA

*: Correspondence should be addressed to Dr. Kai Wang, 1501 San Pablo Street, Los Angeles, CA 90089, USA,

Emails: Fan Gao , Kai Wang

Supplementary information

Supplementary Figure: Density scatterplots of TRBV subtype usage and VJ recombination usage identified in the biological duplicates of normal samples S1 & S2. Pearson’s correlation coefficients were also shown in the plots. Log10(counts+1) values were used for calculation and plotting.

Supplementary Table 1. Demographics of Patients with Meningiomas

Sample ID / Gender / Race / Chemo/ Radiation / WHO Grade / Sample Type
347_B / F / H / NONE / I / Benign
392_B / F / H / NONE / I / Benign
010_M / M / C / NONE / III / Malignant
221_M / M / H / NONE / III / Malignant

Supplementary Table 2. Summary of sequencing data statistics for meningiomas samples

Sample ID / 010_M / 221_M / 347_B / 392_B
Total number of sequenced reads / 36,794,407 / 13,405,950 / 5,807,826 / 9,051,764
Number of reads with P-U end tag / 14,714,739 / 5,540,304 / 1,493,598 / 2,267,131
Number of reads with P-VDJ end tag / 9,933,135 / 5,177,620 / 1,211,356 / 2,777,050
P-U tagged reads containing TRBV (+)* / 2,663,062 / 1,880,539 / 304,399 / 338,750
P-U tagged reads containing TRAV (+) / 347,758 / 44,272 / 33,608 / 44,525
P-U tagged reads containing TRDV (+) / 9,510 / 28,161 / 939 / 689
P-U tagged reads containing TRGV (+) / 208,117 / 105,975 / 56,620 / 18,033
P-VDJ tagged reads containing TRBV (-)* / 5,164,687 / 3,137,902 / 505,981 / 787,828
P-VDJ tagged reads containing TRAV (-) / 916,075 / 638,292 / 135,112 / 410,918
P-VDJ tagged reads containing TRDV (-) / 6,799 / 26,969 / 867 / 13,765
P-VDJ tagged reads containing TRGV (-) / 145,852 / 61,022 / 37,225 / 12,931

*(+) Reads aligned to the coding strand; (-) Reads aligned to the reverse complement strand.

Supplementary Table 3. Summary of V(D)J junction reads for meningiomas samples

Sample ID / 010_M / 221_M / 347_B / 392_B
P-VDJ tagged reads containing productive TRB-V(D)J junctions (-) / 1,177,610 / 1,250,012 / 129,594 / 127,592
P-VDJ tagged reads containing productive TRA-V(D)J junctions (-) / 185,624 / 9,341 / 4,047 / 14,328
P-VDJ tagged reads containing productive TRD-V(D)J junctions (-) / 1,635 / 3,466 / 88 / 186
P-VDJ tagged reads containing productive TRG-V(D)J junctions (-) / 2,750 / 166 / 192 / 260

Supplementary Table 4. Summary of statistics of the 7-million-read sequencing data for meningiomas samples

Sample ID / 010_M (7M reads) / 221_M (7M reads) / 347_B / 392_B
Total number of sequenced reads / 7,000,000 / 7,000,000 / 5,807,826 / 9,051,764
Number of reads with P-U end tag / 2,832,252 / 2,928,413 / 1,493,598 / 2,267,131
Number of reads with P-VDJ end tag / 1,889,027 / 2,712,692 / 1,211,356 / 2,777,050
P-U tagged reads containing TRBV (+)* / 512,879 / 994,352 / 304,399 / 338,750
P-U tagged reads containing TRAV (+) / 67,062 / 22,906 / 33,608 / 44,525
P-U tagged reads containing TRDV (+) / 1,825 / 14,776 / 939 / 689
P-U tagged reads containing TRGV (+) / 39,981 / 55,806 / 56,620 / 18,033
P-VDJ tagged reads containing TRBV (-)* / 979,048 / 1,646,272 / 505,981 / 787,828
P-VDJ tagged reads containing TRAV (-) / 174,039 / 336,225 / 135,112 / 410,918
P-VDJ tagged reads containing TRDV (-) / 1,251 / 14,223 / 867 / 13,765
P-VDJ tagged reads containing TRGV (-) / 27,817 / 32,075 / 37,225 / 12,931

*(+) Reads aligned to the coding strand; (-) Reads aligned to the reverse complement strand.

Supplementary Table 5. Summary of V(D)J junction reads of the 7-million-read sequencing data for meningiomas samples

Sample ID / 010_M (7M reads) / 221_M (7M reads) / 347_B / 392_B
P-VDJ tagged reads containing productive TRB-V(D)J junctions (-) / 224,383 / 651,607 / 129,594 / 127,592
P-VDJ tagged reads containing productive TRA-V(D)J junctions (-) / 34,890 / 4,253 / 4,047 / 14,328
P-VDJ tagged reads containing productive TRD-V(D)J junctions (-) / 294 / 1,799 / 88 / 186
P-VDJ tagged reads containing productive TRG-V(D)J junctions (-) / 486 / 93 / 192 / 260

Supplementary Table 6. Summary of sequencing data statistics for normal samples

Sample ID / S1_rep1 / S1_rep2 / S2_rep1 / S2_rep2
Total number of sequenced reads / 1,741,581 / 541,838 / 1,598,845 / 570,634
Number of reads with P-U end tag / 402,566 / 150,445 / 400,529 / 140,370
Number of reads with P-VDJ end tag / 670,897 / 254,445 / 592,434 / 194,034
P-U tagged reads containing TRBV (+)* / 193,397 / 70,541 / 128,042 / 73,034
P-U tagged reads containing TRAV (+)* / 16,444 / 1,154 / 9,584 / 549
P-U tagged reads containing TRDV (+)* / 11 / 7 / 631 / 19
P-U tagged reads containing TRGV (+)* / 1,320 / 395 / 18,020 / 1,121
P-VDJ tagged reads containing TRBV (-)* / 541,060 / 177,998 / 406,401 / 127,632
P-VDJ tagged reads containing TRAV (-)* / 24,673 / 8,316 / 33,761 / 36,295
P-VDJ tagged reads containing TRDV (-)* / 121 / 80 / 5,831 / 503
P-VDJ tagged reads containing TRGV (-)* / 315 / 94 / 211 / 606

*(+) Reads aligned to the coding strand; (-) Reads aligned to the reverse complement strand.

Supplementary Table 7. Summary of V(D)J junction reads for normal samples

Sample ID / S1_rep1 / S1_rep2 / S2_rep1 / S2_rep2
P-VDJ tagged reads containing productive TRB-V(D)J junctions (-) / 416,296 / 138,374 / 113,830 / 80,757
P-VDJ tagged reads containing productive TRA-V(D)J junctions (-) / 12,330 / 2,346 / 14,530 / 3,492
P-VDJ tagged reads containing productive TRD-V(D)J junctions (-) / 40 / 20 / 35 / 181
P-VDJ tagged reads containing productive TRG-V(D)J junctions (-) / 36 / 10 / 12 / 28

Page 1